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RNA-seq analysis of single bovine blastocysts.

Authors :
Chitwood JL
Rincon G
Kaiser GG
Medrano JF
Ross PJ
Source :
BMC genomics [BMC Genomics] 2013 May 25; Vol. 14, pp. 350. Date of Electronic Publication: 2013 May 25.
Publication Year :
2013

Abstract

Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect.<br />Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant's transcripts.<br />Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.

Details

Language :
English
ISSN :
1471-2164
Volume :
14
Database :
MEDLINE
Journal :
BMC genomics
Publication Type :
Academic Journal
Accession number :
23705625
Full Text :
https://doi.org/10.1186/1471-2164-14-350